No brain scan can tell you what gender you are. Your gender is decided before any brain scan is given. Any method that attempted to correlate a transgender brain to a male or female brain can only ever be deeply flawed and prejudiced.
They acquire the samples that they would be checking you against by taking their genders for granted, so that no matter what any of the women's brains were like, how different they were from other women's brains, the researchers would say "oh, I guess women's brains can be like that too", and add it to the calculated variance that makes up their "female" category, but if a transgender person's brain differs from the samples, then this is apparently evidence of a lack of correlation, or evidence that they aren't female... but if you were already, pre-determined to be female without having to pass any brains scans, then this would be the opposite, and evidence of what a female brain is like, regardless of correlation, or similarity to the brains of others.